Genome-Wide Transcriptome and Expression Profile Analysis of Phalaenopsis during Explant Browning
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{"title"=>"Genome-Wide transcriptome and expression profile analysis of Phalaenopsis during explant browning", "type"=>"journal", "authors"=>[{"first_name"=>"Chuanjun", "last_name"=>"Xu", "scopus_author_id"=>"56164426000"}, {"first_name"=>"Biyu", "last_name"=>"Zeng", "scopus_author_id"=>"56647539700"}, {"first_name"=>"Junmei", "last_name"=>"Huang", "scopus_author_id"=>"56647088600"}, {"first_name"=>"Wen", "last_name"=>"Huang", "scopus_author_id"=>"56799058500"}, {"first_name"=>"Yumei", "last_name"=>"Liu", "scopus_author_id"=>"57192564557"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84929464917", "doi"=>"10.1371/journal.pone.0123356", "issn"=>"19326203", "pui"=>"604108117", "sgr"=>"84929464917", "pmid"=>"25874455"}, "id"=>"98443f14-3cd4-3f1d-9f96-96577da70a96", "abstract"=>"BACKGROUND: Explant browning presents a major problem for in vitro culture, and can lead to the death of the explant and failure of regeneration. Considerable work has examined the physiological mechanisms underlying Phalaenopsis leaf explant browning, but the molecular mechanisms of browning remain elusive. In this study, we used whole genome RNA sequencing to examine Phalaenopsis leaf explant browning at genome-wide level.\\n\\nMETHODOLOGY/PRINCIPAL FINDINGS: We first used Illumina high-throughput technology to sequence the transcriptome of Phalaenopsis and then performed de novo transcriptome assembly. We assembled 79,434,350 clean reads into 31,708 isogenes and generated 26,565 annotated unigenes. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript. Using the transcriptome data as a reference, we next analyzed the differential gene expression of explants cultured for 0, 3, and 6 d, respectively. We then identified differentially expressed genes (DEGs) before and after Phalaenopsis explant browning. We also performed GO, KEGG functional enrichment and Pfam analysis of all DEGs. Finally, we selected 11 genes for quantitative real-time PCR (qPCR) analysis to confirm the expression profile analysis.\\n\\nCONCLUSIONS/SIGNIFICANCE: Here, we report the first comprehensive analysis of transcriptome and expression profiles during Phalaenopsis explant browning. Our results suggest that Phalaenopsis explant browning may be due in part to gene expression changes that affect the secondary metabolism, such as: phenylpropanoid pathway and flavonoid biosynthesis. Genes involved in photosynthesis and ATPase activity have been found to be changed at transcription level; these changes may perturb energy metabolism and thus lead to the decay of plant cells and tissues. This study provides comprehensive gene expression data for Phalaenopsis browning. Our data constitute an important resource for further functional studies to prevent explant browning.", "link"=>"http://www.mendeley.com/research/genomewide-transcriptome-expression-profile-analysis-phalaenopsis-during-explant-browning", "reader_count"=>7, "reader_count_by_academic_status"=>{"Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_user_role"=>{"Researcher"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>1, "Student > Master"=>1, "Professor"=>1, "Unspecified"=>1}, "reader_count_by_subject_area"=>{"Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>5, "Unspecified"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>5}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Brazil"=>1}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2020640"], "description"=>"<p>21, 384 genes were grouped into 45 sub-categories, which were divided into three categories: cellular component, molecular function, biological process.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379565, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g003", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_GO_categories_assigned_to_the_Phalaenopsis_transcriptome_/1379565", "title"=>"Distribution of the GO categories assigned to the <i>Phalaenopsis</i> transcriptome.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020654"], "description"=>"<p>The top 20 most highly represented pathways are shown. A: <i>Phalaenopsis</i> genes mapped in <i>Arabidopsis thaliana</i>, B: Distribution of <i>Phalaenopsis</i> genes in KEGG pathways, C: <i>Phalaenopsis</i> genes mapped in <i>Oryza sativa</i></p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379579, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g007", "stats"=>{"downloads"=>2, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Phalaenopsis_genes_and_distribution_of_Phalaenopsis_genes_mapped_in_mapped_in_Arabidopsis_thaliana_and_Oryza_sativa_among_KEGG_pathways_/1379579", "title"=>"Distribution of <i>Phalaenopsis</i> genes and distribution of <i>Phalaenopsis</i> genes mapped in mapped in <i>Arabidopsis thaliana</i> and <i>Oryza sativa</i> among KEGG pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020635"], "description"=>"<p>The number in the parenthesis presents the number of isoforms.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379561, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Venn_diagram_showing_the_number_DEGs_for_each_comparison_and_the_overlaps_between_three_comparison_groups_/1379561", "title"=>"Venn diagram showing the number DEGs for each comparison and the overlaps between three comparison groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020631"], "description"=>"<p>The number of up(blue)- and down(red)- regulate genes in three groups.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379556, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g001", "stats"=>{"downloads"=>0, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_number_of_up_blue_and_down_red_regulate_genes_in_three_groups_/1379556", "title"=>"The number of up(blue)- and down(red)- regulate genes in three groups.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020665"], "description"=>"<p>Analysis was performed using HMMER with Pfam database.</p><p>Distribution of the top 20 Pfam domains identified in translated <i>Phalaenopsis</i> sequences.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379590, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.t008", "stats"=>{"downloads"=>5, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_top_20_Pfam_domains_identified_in_translated_Phalaenopsis_sequences_/1379590", "title"=>"Distribution of the top 20 Pfam domains identified in translated <i>Phalaenopsis</i> sequences.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020662"], "description"=>"<p>Homology analysis of <i>Phalaenopsis</i> proteome with other plants.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379587, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.t002", "stats"=>{"downloads"=>7, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Homology_analysis_of_Phalaenopsis_proteome_with_other_plants_/1379587", "title"=>"Homology analysis of <i>Phalaenopsis</i> proteome with other plants.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020661"], "description"=>"<p>Assembly of transcriptome of <i>Phalaenopsis</i>.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379586, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.t001", "stats"=>{"downloads"=>6, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assembly_of_transcriptome_of_Phalaenopsis_/1379586", "title"=>"Assembly of transcriptome of <i>Phalaenopsis</i>.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020643"], "description"=>"<p>Each vertical column represented the genes that were dramatically up- (red) or down- regulated (blue) comparing the two groups indicated at the top. Lines to the left showed functional category and GO number. Each color bar represents an individual locus.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379568, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g004", "stats"=>{"downloads"=>6, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Enriched_functional_categories_in_each_of_the_pair_wise_comparison_/1379568", "title"=>"Enriched functional categories in each of the pair-wise comparison.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020656"], "description"=>"<p>Distribution of the top 20 Pfam domains identified in three groups of DEGs.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379581, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g008", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_the_top_20_Pfam_domains_identified_in_three_groups_of_DEGs_/1379581", "title"=>"Distribution of the top 20 Pfam domains identified in three groups of DEGs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020648"], "description"=>"<p>(A: Metabolism, B: Genetic Information Processing, C: Environmental Information Processing, D: Cellular Processes, E: Organismal Systems)</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379573, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g006", "stats"=>{"downloads"=>1, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Classification_of_Phalaenopsis_genes_involved_in_KEGG_pathways_/1379573", "title"=>"Classification of <i>Phalaenopsis</i> genes involved in KEGG pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020664"], "description"=>"<p>Pathway enrichment of DEGs was analysis at P-value<0.05.</p><p>List of important KEGG pathways enrichment analysis of DEGs before and after <i>Phalaenopsis</i> explant browning.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379589, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.t007", "stats"=>{"downloads"=>3, "page_views"=>27, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_List_of_important_KEGG_pathways_enrichment_analysis_of_DEGs_before_and_after_Phalaenopsis_explant_browning_/1379589", "title"=>"List of important KEGG pathways enrichment analysis of DEGs before and after <i>Phalaenopsis</i> explant browning.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020693", "https://ndownloader.figshare.com/files/2020694", "https://ndownloader.figshare.com/files/2020695", "https://ndownloader.figshare.com/files/2020696", "https://ndownloader.figshare.com/files/2020697", "https://ndownloader.figshare.com/files/2020698", "https://ndownloader.figshare.com/files/2020699", "https://ndownloader.figshare.com/files/2020700", "https://ndownloader.figshare.com/files/2020701", "https://ndownloader.figshare.com/files/2020702", "https://ndownloader.figshare.com/files/2020703", "https://ndownloader.figshare.com/files/2020704", "https://ndownloader.figshare.com/files/2020705", "https://ndownloader.figshare.com/files/2020706", "https://ndownloader.figshare.com/files/2020707", "https://ndownloader.figshare.com/files/2020708", "https://ndownloader.figshare.com/files/2020709", "https://ndownloader.figshare.com/files/2020710"], "description"=>"<div><p>Background</p><p>Explant browning presents a major problem for <i>in vitro</i> culture, and can lead to the death of the explant and failure of regeneration. Considerable work has examined the physiological mechanisms underlying <i>Phalaenopsis</i> leaf explant browning, but the molecular mechanisms of browning remain elusive. In this study, we used whole genome RNA sequencing to examine <i>Phalaenopsis</i> leaf explant browning at genome-wide level.</p><p>Methodology/Principal Findings</p><p>We first used Illumina high-throughput technology to sequence the transcriptome of <i>Phalaenopsis</i> and then performed <i>de novo</i> transcriptome assembly. We assembled 79,434,350 clean reads into 31,708 isogenes and generated 26,565 annotated unigenes. We assigned Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations, and potential Pfam domains to each transcript. Using the transcriptome data as a reference, we next analyzed the differential gene expression of explants cultured for 0, 3, and 6 d, respectively. We then identified differentially expressed genes (DEGs) before and after <i>Phalaenopsis</i> explant browning. We also performed GO, KEGG functional enrichment and Pfam analysis of all DEGs. Finally, we selected 11 genes for quantitative real-time PCR (qPCR) analysis to confirm the expression profile analysis.</p><p>Conclusions/Significance</p><p>Here, we report the first comprehensive analysis of transcriptome and expression profiles during <i>Phalaenopsis</i> explant browning. Our results suggest that <i>Phalaenopsis</i> explant browning may be due in part to gene expression changes that affect the secondary metabolism, such as: phenylpropanoid pathway and flavonoid biosynthesis. Genes involved in photosynthesis and ATPase activity have been found to be changed at transcription level; these changes may perturb energy metabolism and thus lead to the decay of plant cells and tissues. This study provides comprehensive gene expression data for <i>Phalaenopsis</i> browning. Our data constitute an important resource for further functional studies to prevent explant browning.</p></div>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379607, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0123356.s001", "https://dx.doi.org/10.1371/journal.pone.0123356.s002", "https://dx.doi.org/10.1371/journal.pone.0123356.s003", "https://dx.doi.org/10.1371/journal.pone.0123356.s004", "https://dx.doi.org/10.1371/journal.pone.0123356.s005", "https://dx.doi.org/10.1371/journal.pone.0123356.s006", "https://dx.doi.org/10.1371/journal.pone.0123356.s007", "https://dx.doi.org/10.1371/journal.pone.0123356.s008", "https://dx.doi.org/10.1371/journal.pone.0123356.s009", "https://dx.doi.org/10.1371/journal.pone.0123356.s010", "https://dx.doi.org/10.1371/journal.pone.0123356.s011", "https://dx.doi.org/10.1371/journal.pone.0123356.s012", "https://dx.doi.org/10.1371/journal.pone.0123356.s013", "https://dx.doi.org/10.1371/journal.pone.0123356.s014", "https://dx.doi.org/10.1371/journal.pone.0123356.s015", "https://dx.doi.org/10.1371/journal.pone.0123356.s016", "https://dx.doi.org/10.1371/journal.pone.0123356.s017", "https://dx.doi.org/10.1371/journal.pone.0123356.s018"], "stats"=>{"downloads"=>63, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Transcriptome_and_Expression_Profile_Analysis_of_Phalaenopsis_during_Explant_Browning/1379607", "title"=>"Genome-Wide Transcriptome and Expression Profile Analysis of <i>Phalaenopsis</i> during Explant Browning", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020646"], "description"=>"<p>The top 20 most highly represented pathways are shown. Analysis was performed using Blast2GO and the KEGG database.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379571, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g005", "stats"=>{"downloads"=>0, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_Phalaenopsis_transcriptome_sequences_among_KEGG_Kyoto_Encyclopedia_of_Genes_and_Genomes_pathways_/1379571", "title"=>"Distribution of <i>Phalaenopsis</i> transcriptome sequences among KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020663"], "description"=>"<p>Assembly of <i>Phalaenopsis</i> expression profiles and mapping to transcriptome.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379588, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.t003", "stats"=>{"downloads"=>6, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Assembly_of_Phalaenopsis_expression_profiles_and_mapping_to_transcriptome_/1379588", "title"=>"Assembly of <i>Phalaenopsis</i> expression profiles and mapping to transcriptome.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-14 03:22:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/2020660"], "description"=>"<p>The genes and transcriptome number: comp 20466 (<i>4CL</i>), comp 20354 (<i>DFR</i>), comp 22408 (<i>CH</i>S), comp 14385 (<i>F3'H</i>), comp 20091 (<i>ATP</i> γ subunite), comp 88972 (<i>ATP</i> α subunite); comp 61111 (<i>psbB</i>), comp 5062 (<i>psbD</i>), comp 14647 (<i>POD</i>), comp 23976 (<i>PAL</i>), comp 19716 (<i>PPO</i>). The left y-axis indicates the FPKM (fragments per kilobase of exon modle per millions mapped reads). In a-f and the relative expression level by qPCR(2ΔΔ ct), is presented as fold- changes in gene expression normalized to the actin gene in g-l.</p>", "links"=>[], "tags"=>["gene expression data", "transcriptome", "Phalaenopsis leaf explant", "pcr", "gene expression changes", "deg", "genome RNA sequencing", "kegg", "expression profile analysis", "gene", "Explant Browning BackgroundExplant", "perturb energy metabolism", "Phalaenopsis explant", "analysis"], "article_id"=>1379585, "categories"=>["Uncategorised"], "users"=>["Chuanjun Xu", "Biyu Zeng", "Junmei Huang", "Wen Huang", "Yumei Liu"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0123356.g009", "stats"=>{"downloads"=>2, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transcript_profile_a_f_and_qPCR_g_l_results_of_selected_genes_during_Phalaenopsis_explant_browning_/1379585", "title"=>"Transcript profile(a-f) and qPCR (g-l) results of selected genes during <i>Phalaenopsis</i> explant browning.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-14 03:22:18"}

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  • {"unique-ip"=>"14", "full-text"=>"25", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"8"}
  • {"unique-ip"=>"11", "full-text"=>"18", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2018", "month"=>"12"}
  • {"unique-ip"=>"9", "full-text"=>"20", "pdf"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"2"}
  • {"unique-ip"=>"11", "full-text"=>"23", "pdf"=>"2", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"3", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"3"}
  • {"unique-ip"=>"8", "full-text"=>"12", "pdf"=>"1", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2019", "month"=>"4"}
  • {"unique-ip"=>"19", "full-text"=>"23", "pdf"=>"4", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"2", "cited-by"=>"0", "year"=>"2019", "month"=>"5"}

Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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